Exploring interactions of endocrine-disrupting compounds with different conformations of the human estrogen receptor alpha ligand binding domain: a molecular docking study

Effect-Targeted Mapping of Potential Estrogenic Agonists and Antagonists in Wastewater via a Conformation-Specific Reporter-Mediated Biosensor

Wastewater treatment plants (WWTPs) are regarded as the main sources of estrogens that reach the aquatic environment. Hence, continuous monitoring of potential estrogenic-active compounds by a biosensor is an appealing approach. However, existing biosensors cannot simultaneously distinguish and quantify estrogenic agonists and antagonists. To overcome the challenge, we developed an estrogen receptor-based biosensor that selectively screened estrogenic agonists and antagonists by introducing rationally designed agonist/antagonist conformation-specific reporters. The double functional conformation-specific reporters consist of a Cy5.5-labeled streptavidin moiety and a peptide moiety, serving as signal recognition and signal transduction elements. In addition, the conformation recognition mechanism was further validated at the molecular level through molecular docking. Based on the two-step "turn-off" strategy, the biosensor exhibited remarkable sensitivity, detecting 17β-estradiol-binding activity equivalent (E2-BAE) at 7 ng/L and 4-hydroxytamoxifen-binding activity equivalent (4-OHT-BAE) at 91 ng/L. To validate its practicality, the biosensor was employed in a case study involving wastewater samples from two full-scale WWTPs across different treatment stages to map their estrogenic agonist and antagonist binding activities. Comparison with the yeast two-hybrid bioassay showed a strong liner relationship (r2 = 0.991, p < 0.0001), indicating the excellent accuracy and reliability of this technology in real applications.

Phthalates - A family of plasticizers, their health risks, phytotoxic effects, and microbial bioaugmentation approaches

Phthalates are a family of reprotoxicant compounds, predominantly used as a plasticizer to improve the flexibility and longevity of consumable plastic goods. After their use these plastic products find their way to the waste disposal sites where they leach out the hazardous phthalates present within them, into the surrounding environment, contaminating soil, groundwater resources, and the nearby water bodies. Subsequently, phthalates move into the living system through the food chain and exhibit the well-known phenomenon of biological magnification. Phthalates as a primary pollutant have been classified as 1B reprotoxicants and teratogens by different government authorities and they have thus imposed restrictions on their use. Nevertheless, the release of these compounds in the environment is unabated. Bioremediation has been suggested as one of the ways of mitigating this menace, but studies regarding the field applications of phthalate utilizing microbes for this purpose are limited. Through this review, we endeavor to make a deeper understanding of the cause and concern of the problem and to find out a possible solution to it. The review critically emphasizes the various aspects of phthalates toxicity, including their chemical nature, human health risks, phytoaccumulation and entry into the food chain, microbial role in phthalate degradation processes, and future challenges.

Tissue distribution and endocrine disruption effects of chronic exposure to pharmaceuticals and personal care products mixture at environmentally relevant concentrations in zebrafish

Pharmaceuticals and personal care products (PPCPs) as emerging contaminants are ubiquitously present in the aquatic environment. Using in vivo and in silico techniques, this study aims to elucidate tissue distribution and endocrine disruption effects of chronic exposure (120 days) to PPCP mixture at environmentally relevant concentrations (ERCs) in adult zebrafish. Results from UHPLC-MS/MS analyses showed elevated distribution of PPCPs in zebrafish tissues in the order of liver > gonad > brain. Upregulation of steroid hormone receptors, both gonadotropin, and steroidogenic genes perturb the HPG axis pathway in females, while male fish exhibited significantly downregulated expressions of vtg, cyp17, and 17βhsd genes with inhibited fecundity. The Spearman correlation indicated a significant positive relationship between PPCPs bioaccumulation and mRNA levels of HPG axis genes. In silico molecular docking (MD) revealed specific amino acid residues of PPCPs binding with zebrafish estrogen receptors. Furthermore, the strongest binding energies of sulfamethoxazole, carbamazepine, and triclosan were discovered in erα and erβ estrogen receptors, confirming PPCPs' xenoestrogenic behavior. To summarize, chronic exposure to ERCs resulted in a high accumulation of PPCPs in the liver and gonad tissues of adult zebrafish, as well as associated perturbed genetic responses. As a result, strict environmental regulations for the disposal of PPCPs should be ensured to protect ecological and public health.

Estrogenic activity of lignin-derivable alternatives to bisphenol A assessed via molecular docking simulations

Lignin-derivable bisphenols are potential alternatives to bisphenol A (BPA), a suspected endocrine disruptor; however, a greater understanding of structure–activity relationships (SARs) associated with such lignin-derivable building blocks is necessary to move replacement efforts forward. This study focuses on the prediction of bisphenol estrogenic activity (EA) to inform the design of potentially safer BPA alternatives. To achieve this goal, the binding affinities to estrogen receptor alpha (ERα) of lignin-derivable bisphenols were calculated via molecular docking simulations and correlated to median effective concentration (EC₅₀) values using an empirical correlation curve created from known EC₅₀ values and binding affinities of commercial (bis)phenols. Based on the correlation curve, lignin-derivable bisphenols with binding affinities weaker than ∼−6.0 kcal mol⁻¹ were expected to exhibit no EA, and further analysis suggested that having two methoxy groups on an aromatic ring of the bio-derivable bisphenol was largely responsible for the reduction in binding to ERα. Such dimethoxy aromatics are readily sourced from the depolymerization of hardwood biomass. Additionally, bulkier substituents on the bridging carbon of lignin-bisphenols, like diethyl or dimethoxy, were shown to weaken binding to ERα. And, as the bio-derivable aromatics maintain major structural similarities to BPA, the resultant polymeric materials should possess comparable/equivalent thermal (e.g., glass transition temperatures, thermal decomposition temperatures) and mechanical (e.g., tensile strength, modulus) properties to those of polymers derived from BPA. Hence, the SARs established in this work can facilitate the development of sustainable polymers that maintain the performance of existing BPA-based materials while simultaneously reducing estrogenic potential.

This article explores lignin-derivable bisphenols as alternatives to bisphenol A – a suspected endocrine disruptor – by investigating their structure-activity relationships with respect to estrogen receptor alpha via molecular docking.

Combined toxicity of endocrine-disrupting chemicals: A review

The combined toxicological assessment provides a realistic approach for hazard evaluation of chemical cocktails that co-existed in the environment. This review provides a holistic insight into the studies highlighting the mixture toxicity of the endocrine-disrupting chemicals (EDCs), especially focusing on the screening of biochemical pathways and other toxicogenetic endpoints. Reviewed literature showed that numerous multiplexed toxicogenomic techniques were applied to determine reproductive effects in vertebrates, but limited studies were found in non-mammalian species after mixture chemical exposure. Further, we found that the experimental design and concentration selection are the two important parameters in mixture toxicity studies that should be time- and cost-effective, highly precise, and environmentally relevant. A summary of EDC mixtures affecting the thyroid axis, estrogen axis, androgen axis, growth stress, and immune system via in vivo bioassays was also presented. It is interesting to mention that majority of estrogenic effects of the mixtures were sex-dependent, particularly observed in male fish as compared to female fish. Further, the androgen axis was perturbed with serious malformations in male rat testis (epididymal or gubernacular lesions, and deciduous spermatids). Also, transgenerational epigenetic effects were promoted in the F₃ and F₄ generations in the form of DNA methylation epimutations in sperm, increasing polycystic ovaries and reducing the offspring. Similarly, increased oxidative stress, high antioxidant enzymatic activities, disturbed estrous cycle, and decreased steroidogenesis were the commonly found effects after acute or chronic exposure to EDC mixtures. Importantly, the concentration addition (CA) and independent action (IA) models became more prevalent and suitable predictive models to unveil the prominence of synergistic estrogenic and anti-androgenic effects of chemical mixtures. More importantly, this review encompasses the research challenges and gaps in the existing knowledge and specific future research perspectives on combined toxicity.

Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals

Background

An individual’s response to environmental exposures varies depending on their genotype, which has been termed the gene-environment interaction. The phenotype of cell exposed can also be a key determinant in the response to physiological cues, indicating that a cell-gene-environment interaction may exist. We investigated whether the cellular environment could alter the transcriptional response to environmental chemicals. Publicly available gene expression array data permitted a targeted comparison of the transcriptional response to a unique subclass of environmental chemicals that alter the activity of the estrogen receptor, xenoestrogens.

Results

Thirty xenoestrogens were included in the analysis, for which 426 human gene expression studies were identified. Comparisons were made for studies that met the predefined criteria for exposure length, concentration, and experimental replicates. The cellular response to the phytoestrogen genistein resulted in remarkably unique transcriptional profiles in breast, liver, and uterine cell-types. Analysis of gene regulatory networks and molecular pathways revealed that the cellular context mediated the activation or repression of functions important to cellular organization and survival, including opposing effects by genistein in breast vs. liver and uterine cell-types. When controlling for cell-type, xenoestrogens regulate unique gene networks and biological functions, despite belonging to the same class of environmental chemicals. Interestingly, the genetic sex of the cell-type also strongly influenced the transcriptional response to xenoestrogens in the liver, with only 22% of the genes significantly regulated by genistein common between male and female cells.

Conclusions

Our results demonstrate that the transcriptional response to environmental chemicals depends on a variety of factors, including the cellular context, the genetic sex of a cell, and the individual chemical. These findings highlight the importance of evaluating the impact of exposure across cell-types, as the effect is responsive to the cellular environment. These comparative genetic results support the concept of a cell-gene-environment interaction.

Chronic thiamethoxam exposure impairs the HPG and HPT axes in adult Chinese rare minnow (Gobiocypris rarus): Docking study, hormone levels, histology, and transcriptional responses

Thiamethoxam has emerged as an environmental contaminant detected in aqueous environments, and its endocrine-disrupting effect at chronic exposure in teleosts remains unknown. In the present study, a docking experiment and an in vivo test were integrated to systematically explore the toxic mechanisms of thiamethoxam in fish. Histological analysis, plasma VTG and hormone level (E2, 11-KT, T3 and T4) determinations, and HPG and HPT gene expression quantification were performed after Chinese rare minnow (Gobiocypris rarus) was exposed to thiamethoxam (0, 0.5, 5, and 50 μg/L) for 90 days. According to the docking study, thiamethoxam had different interactions with ERα, AR and TRα via hydrogen bonding. A decrease in body length and plasma T4 was observed in both genders. The histological damage in liver and delayed gonadal development were observed in both genders at 50 μg/L thiamethoxam treatment. In males, the following HPG axis genes were upregulated: gnrh and cyp19b in the brain; vtg and cyp19a in the liver; and cyp17 and cyp19a in the gonad. In females, erɑ in the liver was significantly upregulated with 0.5 μg/L thiamethoxam treatment, and cyp17 in the gonad was upregulated with all treatment. The suppression of cyp19a, gnrh, cyp11a, and ttr was observed at the concentration of 5 μg/L in the female liver. Taken together, the endocrine system of Chinese rare minnow might be disrupted after chronic exposure to thiamethoxam.

In silico study of molecular mechanisms of action: Estrogenic disruptors among phthalate esters

Phthalate esters (PAEs), as widely used plasticizers, have been concerned for their possible disruption of estrogen functions via binding to and activating the transcription of estrogen receptors (ERs). Nevertheless, the computational interpretation of the mechanism of ERs activities modulated by PAEs at the molecular level is still insufficient, which hinders the reliable screening of the ERs-active PAEs with high speed and high throughput. To bridge the gap, the in silico simulations considering the effects of coactivators were accomplished to explore the molecular mechanism of action for the purpose of predicting the estrogenic potencies of PAEs. The transcriptional activation functions of human ERα (hERα) modulated by PAEs is predicted via the simulations including binding interaction of PAEs and hERα, conformational changes of PAEs-hERα complexes and recruitment of coactivators. Molecular insight into the diverse estrogen mechanism of action among PAEs with regard to hERα agonists and selective estrogen receptor modulators (SERMs) is provided. Agonist-modulated conformational change of hERα leads to the optimal exposure of its Activation Function 2 (AF-2) surface which, in turn, facilitates the recruitment of coactivators, therefore promoting the transcriptional activation functions of hERα. Conversely, binding interaction of hERα with SERMs among PAEs leads to the conformational change with blocked AF-2 surface, thus preventing the recruitment of coactivators and consequently inhibiting the AF-2 activity. The two-hybrid recombinant yeast is experimentally used for verification. The established in silico evaluation methodology exhibits great promise to speed up the prediction of chemicals which work as hERα agonist or SERMs.

Environmental polycyclic aromatic hydrocarbons mixture, in human blood levels, decreased oestradiol secretion by granulosa cells via ESR1 and GPER1 but not ESR2 receptor

Tissue-dependent oestrogenic and anti-oestrogenic activity of polycyclic aromatic hydrocarbons (PAHs) has been suggested. In this study, the effect of two PAH mixtures, M1 composed of all 16 priority pollutants and M2 composed of five (noted in the highest levels) compounds, on follicle-stimulating hormone receptor (FSHR) expression, basal or FSH-induced oestradiol (E2) secretion and aromatase cytochrome P450 (P450arom) protein expression, by non-luteinised human granulosa cell line (HGrC1) was determined. In addition, the consequences of gene silencing of oestrogen receptor alfa (siESR1), oestrogen receptor beta (siESR2) and a G protein-coupled receptor (siGPER1) on the above parameters were described. Neither PAH mixture had an effect on basal FSHR protein expression; however, both mixtures increased FSH-induced FSHR expression. Decreased E2 secretion and P450arom expression was also demonstrated. In both basal and FSH treated cells, siESR1 and siGPER1 reversed the inhibitory effect of the mixtures on E2 secretion; however, in siESR2 cells, the inhibitory effect was still observed. This study showed that both classic ESR1 and GPER1 were involved in the inhibitory effect of both PAH mixtures on E2 secretion and confirmed that expression of P450arom could be downregulated through the aryl hydrocarbon receptor and additionally through the ESR2.

Protonation state effects of estrogen receptor α on the recognition mechanisms by perfluorooctanoic acid and perfluorooctane sulfonate: A computational study

Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) have been reported to cause adverse health effects on wildlife as well as humans. Numerous studies demonstrated that PFOA and PFOS could interfere with the transcriptional activation of estrogen receptor α (ERα) by mimicking the function of endogenous ligand, whereas some reports suggested that the two compounds present non-estrogenic activities. These conflicting results bring a confusion to understand their molecular mechanism on the ERα-mediated signaling pathway. To address this issue, we performed the molecular docking and molecular dynamics simulations to elaborate the structural characteristics for the binding of PFOA and PFOS to ERα. Our results indicated that the two opposite binding orientations were modulated by the protonation states of key residue His524. In sub-acidic condition, PFOA and PFOS prefer to form the H-bonding interactions with the protonated His524, whereas Arg394 provided the H-bonding interactions for stable binding in sub-alkaline condition. Conformational analyses implied that the diverse binding modes were closely related to the conformational propensity of ERα for subsequent coactivator recruitment and transcription activation. Generally, our findings provide a flexible strategy to assess the pH impacts of microenvironment on the toxicities of perfluoroalkyl acids by their interactions with proteins.

Exploring non-linear distance metrics in the structure-activity space: QSAR models for human estrogen receptor

Background

Quantitative structure-activity relationship (QSAR) models are important tools used in discovering new drug candidates and identifying potentially harmful environmental chemicals. These models often face two fundamental challenges: limited amount of available biological activity data and noise or uncertainty in the activity data themselves. To address these challenges, we introduce and explore a QSAR model based on custom distance metrics in the structure-activity space.

Methods

The model is built on top of the k-nearest neighbor model, incorporating non-linearity not only in the chemical structure space, but also in the biological activity space. The model is tuned and evaluated using activity data for human estrogen receptor from the US EPA ToxCast and Tox21 databases.

Results

The model closely trails the CERAPP consensus model (built on top of 48 individual human estrogen receptor activity models) in agonist activity predictions and consistently outperforms the CERAPP consensus model in antagonist activity predictions.

Discussion

We suggest that incorporating non-linear distance metrics may significantly improve QSAR model performance when the available biological activity data are limited.

Electronic supplementary material

The online version of this article (10.1186/s13321-018-0300-0) contains supplementary material, which is available to authorized users.

Diverse pathways of epithelial mesenchymal transition related with cancer progression and metastasis and potential effects of endocrine disrupting chemicals on epithelial mesenchymal transition process

Endocrine disrupting chemicals (EDCs) are natural or synthetic compounds that interfere with normal functions of natural hormones in the body, leading to a disruption of the endocrine system. Specifically, EDCs have the potential to cause formation of several hormone-dependent cancers, including breast, ovarian, and prostate cancers. Epithelial mesenchymal transition (EMT) process by which epithelial cells lose their cell polarity and cell-cell adhesion and acquire mesenchymal phenotype is closely associated with malignant transformation and the initiation of cancer metastasis. As a key epithelial marker responsible for adherens junction, E-cadherin enables the cells to maintain epithelial phenotypes. EMT event is induced by E-cadherin loss which can be carried out by many transcription factors (TFs), including Snail, Slug, ZEB1, ZEB2, Kruppel-like factor 8 (KLF8), and Twist. N-cadherin, fibronectin, and vimentin are mesenchymal markers needed for cellular migration. The EMT process is regulated by several signaling pathways mediated by transforming growth factor β (TGF-β), Wnt-β-catenin, Notch, Hedgehog, and receptor tyrosine kinases. In the present article, we reviewed the current understanding of cancer progression effects of synthetic chemical EDCs such as bisphenol A (BPA), phthalates, tetrachlorodibenzo-p-dioxin (TCDD), and triclosan by focusing their roles in the EMT process. Collectively, the majority of previous studies revealed that BPA, phthalates, TCDD, and triclosan have the potential to induce cancer metastasis through regulating EMT markers and migration via several signaling pathways associated with the EMT program. Therefore, it is considered that the exposure to these EDCs can increase the risk aggravating the disease for the patients suffering cancer and that more regulations about the use of these EDCs are needed.

Integration of in silico methods and computational systems biology to explore endocrine-disrupting chemical binding with nuclear hormone receptors

Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data. In this study, the predictive ability of QSAR and docking approaches is evaluated using these data sets. This study also presents a computational systems biology approach using carbaryl (1-naphthyl methylcarbamate) as a case study. For estrogen receptor and androgen receptor binding predictions, two commercial and two open source QSAR tools were used, as was the publicly available docking tool Endocrine Disruptome. For estrogen receptor binding predictions, the ADMET Predictor, VEGA, and OCHEM models (specificity: 0.88, 0.88, and 0.86, and accuracy: 0.81, 0.84, and 0.88, respectively) were each more reliable than the MetaDrug™ model (specificity 0.81 and accuracy 0.77). For androgen receptor binding predictions, the Endocrine Disruptome and ADMET Predictor models (specificity: 0.94 and 0.8, and accuracy: 0.78 and 0.71, respectively) were more reliable than the MetaDrug™ model (specificity 0.33 and accuracy 0.4). A consensus approach is proposed that reaches general agreement among the models (specificity 0.94 and accuracy 0.89). This study integrates QSAR, docking, and systems biology approaches as a virtual screening tool for use in risk assessment. As such, this systems biology pathways and network analysis approach provides a means to more critically assess the potential effects of endocrine-disrupting chemicals.

Fludioxonil induced the cancer growth and metastasis via altering epithelial-mesenchymal transition via an estrogen receptor-dependent pathway in cellular and xenografted breast cancer models

Fludioxonil is an antifungal agent used in agricultural applications that is present at measurable amounts in fruits and vegetables. In this study, the effects of fludioxonil on cancer cell viability, epithelial-mesenchymal transition (EMT), and metastasis were examined in MCF-7 clonal variant breast cancer cell (MCF-7 CV cells) with estrogen receptors (ERs). MCF-7 CV cells were cultured with 0.1% DMSO (control), 17β-estradiol (E2; 1 ×10^-9 M, positive control), or fludioxonil (10^-5 -10^-8 M). MTT assay revealed that fludioxonil increased MCF-7 CV cell proliferation 1.2 to 1.5 times compared to the control, while E2 markedly increased the cell proliferation by about 3.5 times. When the samples were co-treated with ICI 182,780 (10^-8 M), an ER antagonist, fludioxonil-induced cell proliferation was reversed to the level of the control. Protein levels of cyclin E1, cyclin D1, Snail, and N-cadherin increased in response to fludioxonil as the reaction to E2, but these increases were not observed when fludioxonil was administered with ICI 182,780. Moreover, the protein level of p21 and E-cadherin decreased in response to treatment with fludioxonil, but remained at the control level when co-treated with ICI 182,780. In xenografted mouse models transplanted with MCF-7 CV cells, fludioxonil significantly increased the tumor mass formation by about 2.5 times as E2 did when compared to vehicle (0.1% DMSO) during the experimental period (80 days). Immunohistochemistry revealed that the protein level of proliferating cell nuclear antigen (PCNA), Snail, and cathepsin D increased in response to fludioxonil as the reaction to E2. These results imply that fludioxonil may have a potential to induce growth or metastatic behaviors of breast cancer by regulation of the expression of cell cycle-, EMT-, and metastasis-related genes via the ER-dependent pathway. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1439-1454, 2017.

Molecular Mechanism of Binding between 17β-Estradiol and DNA

Although 17β-estradiol (E2) is a natural molecule involved in the endocrine system, its widespread use in various applications has resulted in its accumulation in the environment and its classification as an endocrine-disrupting molecule. These molecules can interfere with the hormonal system, and have been linked to various adverse effects such as the proliferation of breast cancer. It has been proposed that E2 could contribute to breast cancer by the induction of DNA damage. Mass spectrometry has demonstrated that E2 can bind to DNA but the mechanism by which E2 interacts with DNA has yet to be elucidated. Using all-atom molecular dynamics simulations, we demonstrate that E2 intercalates (inserts between two successive DNA base pairs) in DNA at the location specific to estrogen receptor binding, known as the estrogen response element (ERE), and to other random sequences of DNA. Our results suggest that excess E2 has the potential to disrupt processes in the body which rely on binding to DNA, such as the binding of the estrogen receptor to the ERE and the activity of enzymes that bind DNA, and could lead to DNA damage.

Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action

Molecular modeling has become an essential tool in predicting and simulating endocrine disrupting effects of chemicals. A key prerequisite for successful application of molecular modeling lies in the correctness of 3D structure for biomacromolecules to be simulated. To date, there are several databases that can provide the experimentally-determined 3D structures. However, commonly, there are many challenges or disadvantageous factors, e.g., (a) lots of 3D structures for a given biomacromolecular target in the protein database; (b) the quality variability for those structures; (c) belonging to different species; (d) mutant amino acid residue in key positions, and so on. Once an inappropriate 3D structure of a target biomacromolecule was selected in molecular modeling, the accuracy and scientific nature of the modeling results could be inevitably affected. In this article, based on literature survey and an analysis of the 3D structure characterization of biomacromolecular targets belonging to the endocrine system in protein databases, six principles were proposed to guide the selection of the appropriate 3D structure of biomacromolecules. The principles include considering the species diversity, the mechanism of action, whether there are mutant amino acid residues, whether the number of protein chains is correct, the degree of structural similarity between the ligand in 3D structure and the target compounds, and other factors, e.g., the experimental pH conditions of the structure determined process and resolution.

Artonin E and Structural Analogs from Artocarpus Species Abrogates Estrogen Receptor Signaling in Breast Cancer

The increasing rate of mortality ensued from breast cancer has encouraged research into safer and efficient therapy. The human Estrogen receptor α has been implicated in the majority of reported breast cancer cases. Molecular docking employing Glide, Schrodinger suite 2015, was used to study the binding affinities of small molecules from the Artocarpus species after their drug-like properties were ascertained. The structure of the ligand-binding domain of human Estrogen receptor α was retrieved from Protein Data Bank while the structures of compounds were collected from PubChem database. The binding interactions of the studied compounds were reported as well as their glide scores. The best glide scored ligand, was Artonin E with a score of -12.72 Kcal when compared to other studied phytomolecules and it evoked growth inhibition of an estrogen receptor positive breast cancer cells in submicromolar concentration (3.8-6.9 µM) in comparison to a reference standard Tamoxifen (18.9-24.1 µM) within the tested time point (24-72 h). The studied ligands, which had good interactions with the target receptor, were also drug-like when compared with 95% of orally available drugs with the exception of Artoelastin, whose predicted physicochemical properties rendered it less drug-like. The in silico physicochemical properties, docking interactions and growth inhibition of the best glide scorer are indications of the anti-breast cancer relevance of the studied molecules.

Use of computational modeling approaches in studying the binding interactions of compounds with human estrogen receptors

Estrogens have a whole host of physiological functions in many human organs and systems, including the reproductive, cardiovascular, and central nervous systems. Many naturally-occurring compounds with estrogenic or antiestrogenic activity are present in our environment and food sources. Synthetic estrogens and antiestrogens are also important therapeutic agents. At the molecular level, estrogen receptors (ERs) mediate most of the well-known actions of estrogens. Given recent advances in computational modeling tools, it is now highly practical to use these tools to study the interaction of human ERs with various types of ligands. There are two common categories of modeling techniques: one is the quantitative structure activity relationship (QSAR) analysis, which uses the structural information of the interacting ligands to predict the binding site properties of a macromolecule, and the other one is molecular docking-based computational analysis, which uses the 3-dimensional structural information of both the ligands and the receptor to predict the binding interaction. In this review, we discuss recent results that employed these and other related computational modeling approaches to characterize the binding interaction of various estrogens and antiestrogens with the human ERs. These examples clearly demonstrate that the computational modeling approaches, when used in combination with other experimental methods, are powerful tools that can precisely predict the binding interaction of various estrogenic ligands and their derivatives with the human ERs.

Application of Circular Dichroism Spectroscopy to the Analysis of the Interaction Between the Estrogen Receptor Alpha and Coactivators: The Case of Calmodulin

The estrogen receptor α ligand-binding domain (ERα-LBD) binds the natural hormone 17β-estradiol (E2) to induce transcription and cell proliferation. This process occurs with the contribution of protein and peptide partners (also called coactivators) that can modulate the structure of ERα, and therefore its specificity of action. As with most transcription factors, ERα exhibits a high content of α helix, making it difficult to routinely run spectroscopic studies capable of deciphering the secondary structure of the different partners under binding conditions. Ca(2+)-calmodulin, a protein also highly structured in α-helix, is a key coactivator for ERα activity. Here, we show how circular dichroism can be used to study the interaction of ERα with Ca(2+)-calmodulin. Our approach allows the determination not only of the conformational changes induced upon complex formation but also the dissociation constant (K d) of this interaction.

A monograph on the remediation of hazardous phthalates

Phthalates or phthalic acid esters are a group of xenobiotic and hazardous compounds blended in plastics to enhance their plasticity and versatility. Enormous quantities of phthalates are produced globally for the production of plastic goods, whose disposal and leaching out into the surroundings cause serious concerns to the environment, biota and human health. Though in silico computational, in vitro mechanistic, pre-clinical animal and clinical human studies showed endocrine disruption, hepatotoxic, teratogenic and carcinogenic properties, usage of phthalates continues due to their cuteness, attractive chemical properties, low production cost and lack of suitable alternatives. Studies revealed that microbes isolated from phthalate-contaminated environmental niches efficiently bioremediate various phthalates. Based upon this background, this review addresses the enumeration of major phthalates used in industry, routes of environmental contamination, evidences for health hazards, routes for in situ and ex situ microbial degradation, bacterial pathways involved in the degradation, major enzymes involved in the degradation process, half-lives of phthalates in environments, etc. Briefly, this handy module would enable the readers, environmentalists and policy makers to understand the impact of phthalates on the environment and the biota, coupled with the concerted microbial efforts to alleviate the burden of ever increasing load posed by phthalates.

Effect of fenhexamid and cyprodinil on the expression of cell cycle- and metastasis-related genes via an estrogen receptor-dependent pathway in cellular and xenografted ovarian cancer models

Fenhexamid and cyprodinil are antifungal agents (pesticides) used for agriculture, and are present at measurable amounts in fruits and vegetables. In the current study, the effects of fenhexamid and cyprodinil on cancer cell proliferation and metastasis were examined. Additionally, the protein expression levels of cyclin D1 and cyclin E as well as cathepsin D were analyzed in BG-1 ovarian cancer cells that express estrogen receptors (ERs). The cells were cultured with 0.1% dimethyl sulfoxide (DMSO; control), 17β-estradiol (E2; 10(-9)M), and fenhexamid or cyprodinil (10(-5)-10(-7)M). Results of a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay showed that fenhexamid and cyprodinil increased BG-1 cell proliferation about 1.5 to 2 times similar to E2 (5 times) compared to the control. When the cells were co-treated with ICI 182,780 (10(-8)M), an ER antagonist, the proliferation of pesticide-treated BG-1 cells was decreased to the level of the control. A wound healing assay revealed that the pesticides reduced the disrupted area in the BG-1 cell monolayer similar to E2. Protein levels of cyclin D1 and E as well as cathepsin D were increased by fenhexamid and cyprodinil. This effect was reversed by co-treatment with ICI 182,780. In a xenograft mouse model with transplanted BG-1 cells, cyprodinil significantly increased tumor mass formation about 2 times as did E2 (6 times) compared to the vehicle (0.1% DMSO) over an 80-day period. In contrast, fenhexamid did not promote ovarian tumor formation in this mouse model. Cyprodinil also induced cell proliferation along with the expression of proliferating cell nuclear antigen (PCNA) and cathepsin D in tumor tissues similar to E2. Taken together, these results imply that fenhexamid and cyprodinil may have disruptive effects on ER-expressing cancer by altering the cell cycle- and metastasis-related gene expression via an ER-dependent pathway.

Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors.

Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations

ERα dimer formation reshapes the helix 12 conformational landscape and is a leading factor for the activation helix conformation.

Atomic insights into distinct hormonal activities of Bisphenol A analogues toward PPARγ and ERα receptors

Bisphenol A analogues (BPAs) belong to a wide variety of large volume chemicals with diverse applications yet emerging environmental concerns. Limited experimental data have demonstrated that BPAs with different halogenation patterns distinctly affect the agonistic activities toward proliferator-activated receptor (PPAR)γ and estrogen receptors (ER)α. Understanding the modes of action of BPAs toward different receptors is essential, however, the underlying molecular mechanism is still poorly understood. Here we probed the molecular recognition process of halogenated BPAs including TBBPA, TCBPA, BPAF, BPC, triBBPA, diBBPA, and monoBBPA toward PPARγ and ERα by molecular modeling, especially the impact of different halogen patterns. Increasing bromination at phenolic rings of BPAs was found highly correlated with electrostatic interactions (R(2) = 0.978 and 0.865 toward PPARγ and ERα, respectively) and van der Waals interactions (R(2) = 0.995 and 0.994 toward PPARγ and ERα, respectively). More halogenated phenolic rings at 3,5-positions of BPAs increase the shielding of the hormonally active phenolic OH and markedly decrease electrostatic interactions favorable for agonistic activities toward PPARγ, but unfavorable for agonistic activities toward ERα. The halogenation at the phenolic rings of BPAs exerts more impact on molecular electrostatic potential distribution than halogenation at the bridging alkyl moiety. Different halogenations further alter hydrogen bond interactions of BPAs and induce conformational changes of PPARγ ligand binding domain (LBD) and ERα LBD, specifically affecting the stabilization of helix H12 attributable to the different agonistic activities. Our results indicate that structural variations in halogenation patterns result in different interactions of BPAs with PPARγ LBD and ERα LBD, potentially causing distinct agonistic/antagonistic toxic effects. The various halogenation patterns should be fully considered for the design of future environmentally benign chemicals with reduced toxicities and desired properties.

Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches

Identification of endocrine disrupting chemicals is one of the important goals of environmental chemical hazard screening. We report on the development of validated in silico predictors of chemicals likely to cause estrogen receptor (ER)-mediated endocrine disruption to facilitate their prioritization for future screening. A database of relative binding affinity of a large number of ERα and/or ERβ ligands was assembled (546 for ERα and 137 for ERβ). Both single-task learning (STL) and multi-task learning (MTL) continuous quantitative structure-activity relationship (QSAR) models were developed for predicting ligand binding affinity to ERα or ERβ. High predictive accuracy was achieved for ERα binding affinity (MTL R(2)=0.71, STL R(2)=0.73). For ERβ binding affinity, MTL models were significantly more predictive (R(2)=0.53, p<0.05) than STL models. In addition, docking studies were performed on a set of ER agonists/antagonists (67 agonists and 39 antagonists for ERα, 48 agonists and 32 antagonists for ERβ, supplemented by putative decoys/non-binders) using the following ER structures (in complexes with respective ligands) retrieved from the Protein Data Bank: ERα agonist (PDB ID: 1L2I), ERα antagonist (PDB ID: 3DT3), ERβ agonist (PDB ID: 2NV7), and ERβ antagonist (PDB ID: 1L2J). We found that all four ER conformations discriminated their corresponding ligands from presumed non-binders. Finally, both QSAR models and ER structures were employed in parallel to virtually screen several large libraries of environmental chemicals to derive a ligand- and structure-based prioritized list of putative estrogenic compounds to be used for in vitro and in vivo experimental validation.

Assessment and molecular actions of endocrine-disrupting chemicals that interfere with estrogen receptor pathways

In all vertebrate species, estrogens play a crucial role in the development, growth, and function of reproductive and nonreproductive tissues. A large number of natural or synthetic chemicals present in the environment and diet can interfere with estrogen signaling; these chemicals are called endocrine disrupting chemicals (EDCs) or xenoestrogens. Some of these compounds have been shown to induce adverse effects on human and animal health, and some compounds are suspected to contribute to diverse disease development. Because xenoestrogens have varying sources and structures and could act in additive or synergistic effects when combined, they have multiple mechanisms of action. Consequently, an important panel of in vivo and in vitro bioassays and chemical analytical tools was used to screen, evaluate, and characterize the potential impacts of these compounds on humans and animals. In this paper, we discuss different molecular actions of some of the major xenoestrogens found in food or the environment, and we summarize the current models used to evaluate environmental estrogens.

Distinct mechanisms of endocrine disruption of DDT-related pesticides toward estrogen receptor α and estrogen-related receptor γ

Dichlorodiphenyltrichloroethane (DDT) is ubiquitous in the environment, and the exposure to DDT and its related pesticides has long been linked to endocrine disruption. The mechanism of endocrine disruption toward targeted receptors, however, remains unclear. Probing the molecular recognition of DDT analogs by targeted receptors at the atomic level is critical for deciphering this mechanism. Molecular dynamics (MD) simulations were applied to probe the molecular recognition process of DDT and its five analogs, including dichlordiphenyldichloroethylene (DDE), dichlorodiphenyldichloroethane (DDD), methoxychlor (MXC), p,p'-hydroxy-DDT (HPTE), and dicofol by human estrogen receptor (ER) α and human ER-related receptor (ERR) γ. Van der Waals interactions mainly drive the interactions of DDT analogs with ERα ligand-binding domain (LBD) and ERRγ LBD. Minor structural changes of DDT analogs in the number and position of chlorine and phenolic hydroxyl moiety cause differences in binding modes through aromatic stacking and hydrogen bonding and thus affect differently conformational changes of ERα LBD and ERRγ LBD. The binding of DDT analogs affects the helix 12 orientation of ERα LBD but causes no rearrangement of helix 12 of ERRγ LBD. These results extend our understanding of how DDT analogs exert their estrogen-disrupting effects toward different receptors via multiple mechanisms.

Docking and QSAR study on the binding interactions between polycyclic aromatic hydrocarbons and estrogen receptor

Little is known about the estrogenic activities of polycyclic aromatic hydrocarbons (PAHs) and the underlying mechanisms on estrogenic activities are still unclear. Molecular docking and quantitative structure-activity relationship (QSAR) were used to understand the relationship between molecular structural features and estrogenic activity, and to predict the binding affinity of PAHs to estrogen receptor α (ERα). From molecular docking analysis, hydrogen bonding as well as hydrophobic and π interactions were found between PAHs and ERα. Based on the docking results, appropriate molecular structural parameters were adopted to develop a QSAR model. Five descriptors were included in the QSAR model, which indicated that the estrogenic activity was related to molecular size, van der Waals volumes, shape profiles, polarizabilities and electropological states were significant parameters explaining the estrogenicity. Comparatively, the developed QSAR model had good robustness, predictive ability and mechanistic interpretability. Moreover, the applicability domain of the model was described.

Evaluation of the OECD (Q)SAR Application Toolbox for the profiling of estrogen receptor binding affinities

The determination of binding affinities for the estrogen receptor (ER) is used extensively to assess potential hazards to human health and the environment arising from chemicals that can interfere with natural hormone homeostasis. Given the great number of chemicals to which humans and wildlife are exposed, (quantitative) structure-activity relationship (Q)SAR models for the characterization of ER disruptors represent a fast and cost-efficient alternative to experimental testing. In this toxicological context, the freely available Organisation for Economic Co-operation and Development (OECD) (Q)SAR Application Toolbox provides a profiler for the categorical profiling of chemicals according to their ER binding propensities. The aim of this study was to evaluate the predictive performances of this profiler. To achieve such a purpose, prediction results with the ER-profiler were compared with experimental binding affinities relative to two large datasets of chemicals (rat and human). The resulting Cooper statistics indicated that the binding affinities of the majority of chemicals included in the retained datasets could be correctly predicted.

Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery

As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.

Comparative analysis of binding affinities between styrene and mammalian CYP2E1 by bioinformatics approaches

Cytochrome P450 2E1 (CYP2E1) is a cytochrome P450 enzyme involved in styrene metabolism. This study compared the binding affinities between styrene and 11 mammalian CYP2E1 systems using bioinformatics methods. Firstly, amino acid sequences of CYP2E1s were obtained from the Swiss-Prot database. Then, taking the crystal structure of human CYP2E1 as a template, 3D models of the CYP2E1s of other mammals were constructed using the SWISS-MODEL program. Finally, the generated homology models were applied to calculate their docking capacities against styrene and polystyrene using the Surflex-Dock program, which could automatically dock ligands into a receptor's ligand binding site using a protomol based approach and assess the affinity by an empirically derived scoring function. Docking experiments showed that the studied mammalian CYP2E1s had high binding affinities with styrene. For polystyrene, the dimmer of styrene has high binding affinities with CYP2E1s, however, trimer and other high polymers were found hard to be docked into the CYP2E1s. The results of this study indicated that bioinformatics approaches might be useful tools to predict styrene and polystyrene affinities with mammalian CYP2E1s.

Quantitative determination of bisphenol A from human saliva using bulk derivatization and trap-and-elute liquid chromatography coupled to electrospray ionization mass spectrometry

Endocrine disruptors cause adverse health effects as a result of their ability to shift the hormonal balance that is essential to the body. Bisphenol A (BPA) is an endocrine disruptor that has garnered much attention because of its presence in many consumer materials, which generates a significant risk for exposure. A method is presented for rapid detection of oral exposure to BPA directly from human saliva. Saliva was chosen because it serves as a noninvasive sampling route to detect BPA exposure; however, it is one of many complex biological matrices that have traditionally posed problems in quantitative analysis. Such analyses usually require extensive sample preparation to reduce interferences contributed by the sample matrix. Three validated methods are presented here that feature a streamlined sample-preparation strategy (bulk derivatization) prior to accurate and sensitive analysis by trap-and-elute liquid chromatography coupled to electrospray ionization mass spectrometry. Validated methods include standard addition calibration with variable injection volumes and multiple injection loading, as well as with incorporation of an internal standard. Reported limits of detection reached as low as 49.0 pg/ml (2.9 pg loaded on-column; equivalent to parts per trillion in saliva) among the presented methods with good accuracy and precision throughout. A proof-of-concept study is demonstrated to show that the final validated method has potential application to specific studies for trace-level BPA detection from real samples.

Estrogenic activity of bisphenol A and 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE) demonstrated in mouse uterine gene profiles

BACKGROUND

Interest and concern regarding potentially estrogenic substances have resulted in development of model systems to evaluate mechanisms of such chemicals. Microarray studies have indicated that estradiol (E2)-stimulated uterine responses can be divided into early and late phases. Comparison of E2 uterine transcript profiles and those of other estrogenic chemicals of interest in vivo indicates mechanisms and activities of test compounds.

OBJECTIVES

We compared transcript responses and mechanisms of response using mouse reproductive tracts after treatment with E2, estriol (E3), bisphenol A (BPA), and 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE).

METHODS

Uterine RNA from ovariectomized wild-type mice, estrogen receptor α (ERα) knockout (αERKO) mice, and mice expressing a DNA-binding-deficient ERα (KIKO) treated with E2, E3, BPA, or HPTE for 2 or 24 hr was analyzed by microarray. Resulting regulated transcripts were compared by hierarchical clustering and correlation analysis, and response patterns were verified by reverse-transcription real-time polymerase chain reaction (RT-PCR).

RESULTS

Both xenoestrogens, BPA and HPTE, showed profiles highly correlated to that of E2 in the early response phase (2 hr), but the correlation diminished in the later response phase (24 hr), similar to the known weak estrogen E3. Both xenoestrogens also mimicked E2 in samples from KIKO mice, indicating that they are able to utilize the indirect tethering mode of ERα signaling. No response was detected in ERα-null uteri, indicating that ERα mediates the responses.

CONCLUSION

Our study forms a basis on which patterns of response and molecular mechanisms of potentially estrogenic chemicals can be assessed.

An interpretation of positional displacement of the helix12 in nuclear receptors: preexistent swing-up motion triggered by ligand binding

Positional displacement of helix12 (H12) in the estrogen receptor alpha, which belongs to the nuclear receptor (NR) superfamily, is studied by the molecular dynamics (MD) simulation and the linear response theory. Tendency of the H12 to swing up upon ligand binding, which is consistent with X-ray structures and earlier MD simulations, is reproduced by the calculation of the conformational fluctuation in apo state and the response to the external perturbation. Our study thus provides an interpretation of the positional change of the H12 such that it is derived by the preexistent swing-up motion where the ligand binding works only as a trigger. Our finding, which illustrates underlying mechanism of the H12 motion, would contribute to finding a way to regulate the transcriptional activity by synthesized ligands because the transcriptional activity of the NR is governed by the position of the H12.

Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors' ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Exploring the binding features of polybrominated diphenyl ethers as estrogen receptor antagonists: docking studies

The polybrominated diphenyl ethers (PBDEs) accumulating in nature are known to be endocrine-disrupting compounds. Of first concern are those interacting with and altering activity of the human estrogen receptor alpha (hERalpha). In this study a docking study was carried out to explore the binding modes of PBDE compounds as hERalpha antagonists. It was found that some of the PBDE compounds with antiestrogenic activity extended into the channel of the estrogen receptor (ER), which is usually occupied by the alkylamine side chain of the ER antagonists raloxifene (RAL) and 4-hydroxytamoxifen (OHT), while most PBDE compounds without antiestrogenic activity adopted binding modes similar to that of ER agonist 17beta-estradiol (E2), located in the binding cavity and which did not protrude into the channel. The present study suggests that pose comparison based on docking is useful for discriminating whether or not PBDE compounds have antiestrogenic activity. Knowing the binding modes of compounds in hERalpha can help to screen out antiestrogenic compounds and further develop descriptive and predictive models in ecotoxicology.

A structural view of nuclear hormone receptor: endocrine disruptor interactions

Endocrine-disrupting chemicals (EDCs) represent a broad class of exogenous substances that cause adverse effects in the endocrine system by interfering with hormone biosynthesis, metabolism, or action. The molecular mechanisms of EDCs involve different pathways including interactions with nuclear hormone receptors (NHRs) which are primary targets of a large variety of environmental contaminants. Here, based on the crystal structures currently available in the Protein Data Bank, we review recent studies showing the many ways in which EDCs interact with NHRs and impact their signaling pathways. Like the estrogenic chemical diethylstilbestrol, some EDCs mimic the natural hormones through conserved protein-ligand contacts, while others, such as organotins, employ radically different binding mechanisms. Such structure-based knowledge, in addition to providing a better understanding of EDC activities, can be used to predict the endocrine-disrupting potential of environmental pollutants and may have applications in drug discovery.

Molecular docking and comparative molecular similarity indices analysis of estrogenicity of polybrominated diphenyl ethers and their analogues

Molecular docking and three-dimensional quantitative structure-activity relationships (3D-QSAR) were used to develop models to predict estrogenicity of polybrominated diphenyl ethers (PBDEs), para-hydroxylated polybrominated diphenyl ethers (para-HO-PBDEs), and brominated bisphenol A compounds to the human estrogen receptor alpha (hERalpha). Based on the molecular conformations developed from the molecular docking, predictive comparative molecular similarity indices analysis (CoMSIA) models were developed. The results of CoMSIA modeling with region focusing included were: leave-one-out (LOO) cross-validated coefficient q(2)(LOO) = 0.722 (all 26 compounds), q(2)(LOO) = 0.633 (the training set, 20 compounds), q(2)(LMO, two groups) = 0.520 +/- 0.155 (26 compounds), q(2)(LMO, five groups) = 0.665 +/- 0.068 (26 compounds), predictive r(2), r(2)(pred) = 0.686 (the test set, 6 compounds), and Q(2)(EXT) = 0.678. The 3D-QSAR can be used to infer the activities of compounds with similar structural characteristics. The interaction mechanism between compounds and the hERalpha was explored. Hydrogen bonding of the compound with Glu353 in the hERalpha is an important determinant of the estrogenic activity of para-HO-PBDEs and brominated bisphenol A.

Exploration of endocrine-disrupting chemicals on estrogen receptor alpha by the agonist/antagonist differential-docking screening (AADS) method: 4-(1-adamantyl)phenol as a potent endocrine disruptor candidate

We established a novel screening method to survey endocrine-disrupting chemicals by means of in silico docking calculations. Endocrine disruptors target the human nuclear receptor, which bind a chemical in a pocket presenting in the ligand-binding domain (LBD). The LBD alters its conformation, depending upon the binding of either agonist or antagonist. We discovered that the chemicals can be differentiated into either agonist or antagonist by the docking calculations of the chemical for the LBD. We used the crystal structures of both agonist-bound LBDs and antagonist-bond LBDs as templates in the docking calculations, and estimated binding energies to discriminate between agonist and antagonist bindings. This agonist/antagonist differential-docking screening (AADS) method predicted, for example, 4-(1-adamantyl)phenol as an agonist of the human estrogen receptor alpha (hERalpha). Indeed, this compound, one of the essential raw materials for nanoporous organosilicate thin films, was confirmed to exhibit strong agonist activity in the reporter-gene assay for hERalpha with a high binding affinity. The AADS method is an approach that appears to foresee both the binding ability and the agonist/antagonist function of chemicals for the target nuclear receptors.